# Pulling a skull from MR
**URL:** https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351
**Category:** Support
**Created:** [September 12, 2024, 3:45pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351 "2024-09-12T15:45:35Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@BDhoth](https://discourse.slicer.org/u/BDhoth)
#### Post date: [September 12, 2024, 3:45pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/1 "2024-09-12T15:45:35Z")
Are there any tips for pulling a skull from MRI images? In this sequence the skull is very comparable in the number as other brain matter/soft tissue.
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [September 13, 2024, 3:50am UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/2 "2024-09-13T03:50:37Z")
I woild recommend the HDBrainExtraction extension for skull stripping. See some more details in this recent discussion:
> [@Brain Segmentation in MR](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/6):
>
> It looks like you correctly created a brain mask segmentation in white, and a new skull-stripped volume. The green segment looks like it is from a different segmentation node created from threshold of the image before skull stripping. If you go back to the data view, you can turn off the node named ‘Segmentation’ with the green head label to see only the brain mask label in white.
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### Author:  [@BDhoth](https://discourse.slicer.org/u/BDhoth)
#### Post date: [September 13, 2024, 5:18pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/3 "2024-09-13T17:18:13Z")
I use the HD brain extraction to get a brain segmentation, but this can be used to KEEP only the skull??
Thank you!
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [September 13, 2024, 6:51pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/4 "2024-09-13T18:51:54Z")
Yes, sure, you can blank out the brain region by a few clicks.
- Create `Brain segmentation` output in `HD Brain Extraction Tool` module
- Go to `Segment Editor` module
- Click `Mask volume` effect, `Fill inside`, and `Apply`
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### Author:  [@BDhoth](https://discourse.slicer.org/u/BDhoth)
#### Post date: [October 4, 2024, 12:24pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/5 "2024-10-04T12:24:44Z")
I tried this option, but it doesn’t work the best for getting only the skull. When thresholding it merges right with how it was masked. ANy other options to get a skull only, no soft tissue? Thank you for your help!
Becky
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### Author:  [@nadayoda59](https://discourse.slicer.org/u/nadayoda59)
#### Post date: [January 3, 2025, 1:02am UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/6 "2025-01-03T01:02:34Z")
Have you solved this problem? If you have, please share your method. Thank you.
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### Author:  [@BDhoth](https://discourse.slicer.org/u/BDhoth)
#### Post date: [January 3, 2025, 1:04pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/7 "2025-01-03T13:04:34Z")
No, I have not in a simple way besides going almost slice by slice and interpolating the slices.
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### Author:  [@jonel](https://discourse.slicer.org/u/jonel)
#### Post date: [November 11, 2025, 8:31pm UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/8 "2025-11-11T20:31:09Z")
If you are still searching for a solution to this problem you might be interested in the new ModalityConverter extension: [New extension: ModalityConverter - bringing AI medical image-to-image translation to 3D Slicer](https://discourse.slicer.org/t/new-extension-modalityconverter-bringing-ai-medical-image-to-image-translation-to-3d-slicer/44405) You can use it to generate a synthetic CT from your MRI images, from which you can then easily extract the skull with the Segment Editor.
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### Author:  [@ciro.raggio](https://discourse.slicer.org/u/ciro.raggio)
#### Post date: [March 13, 2026, 7:52am UTC](https://discourse.slicer.org/t/pulling-a-skull-from-mr/38351/9 "2026-03-13T07:52:22Z")
Yes, and here you can also find a [video tutorial](https://github.com/ciroraggio/SlicerModalityConverter?tab=readme-ov-file#skull-extraction-from-t1w-mri-via-deep-learning-based-image-to-image-translation-in-3d-slicer) on how to do it!